* Fix an out of bounds access when replacing fragments
* Add segfaulting US patent CDXs
* Return false when we can't find the bond idx for better handling
* Remove useless REQUIRE
* Only sniff when in format AUTO
* Add test for reading wrong format
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* Fist pass at CDX support
* Enable CDX support for reading (also) in the CDXMLParser API
* Add cdxml test files
* Update swig wrappers for CDXMLFormat and Parameters
* Add constructor to ChemDrawParserParams
* Add Java SWIG support for ChemDraw
* Add chemdraw define to rdconfig
* Add missing chemdraw deps
* Remove direct expat link
* Fix Java linkages for ChemDraw
* Remove bad merge code
* Remove bad merge code
* Fix csharp builds
* Add sniffer for the ChemDraw DataStream
* Include filesystem
* Fix test on windows
* Add more CDX tests
* Ensure streams are open in binary mode to support CDX on windows
* Fix text to show that a Block is the text input, not a file
* Fix CSharp test
* Disable CDX tests when not building chemdraw
* Turn back on chemdraw
* Response to review
* Turn off chemdraw support for the limited external test
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* ChemDraw Document and read/write support for the RDKit
* Add missing test file
* Rev chemdraw version
* Rev chemdraw version
* Rev chemdraw version for g++11
* Update CMakeLists.txt
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Build chemdraw from an external CMake file
* Remove unused platform bigendian check
* Revert changes to constants, remove unused ones
* Keep the original constant names
* Remove __main__ section
* Use as much of the ChemDraw CMakeList as possible
* Skip installing expat
* Rev chemdraw version to fix windows issue
* Don't install expat, set the appropriate CHEMDRAW_BUILD definition
* resolve windows builds
* Fix minimal lib builds
* Move ChemDraw document to private header
* Move utility functions to ChemDraw namespace
* Move ChemDraw to v2 unique ptr api namespace
* Make class enum
* Switch to camelCase
* Response to review
* Move ChemDrawToDocument to ChemDraw namespace
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix typo
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add better documentation
* Rev chemdraw version
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* ChemDraw Document and read/write support for the RDKit
* Add missing test file
* Rev chemdraw version
* Rev chemdraw version
* Rev chemdraw version for g++11
* Update CMakeLists.txt
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Build chemdraw from an external CMake file
* Remove unused platform bigendian check
* Revert changes to constants, remove unused ones
* Keep the original constant names
* Remove __main__ section
* Use as much of the ChemDraw CMakeList as possible
* Skip installing expat
* Rev chemdraw version to fix windows issue
* Don't install expat, set the appropriate CHEMDRAW_BUILD definition
* resolve windows builds
* Fix minimal lib builds
* Move ChemDraw document to private header
* Move utility functions to ChemDraw namespace
* Move ChemDraw to v2 unique ptr api namespace
* Make class enum
* Switch to camelCase
* Response to review
* Move ChemDrawToDocument to ChemDraw namespace
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix typo
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add better documentation
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
